Nucleosides, Nucleotides & Nucleic Acids最新文献_第7页

An improved synthesis of guanosine TNA phosphoramidite for oligonucleotide synthesis. 用于寡核苷酸合成的鸟苷 TNA 亚磷酰胺的改进合成法。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2025-01-01 Epub Date: 2024-06-21 DOI: 10.1080/15257770.2024.2369688

Biju Majumdar, Daisy Sarma, Erica M Lee, Noah A Setterholm, John C Chaput

引用次数: 0

Protective effect of FKBP12 on dextran sulfate sodium-induced ulcerative colitis in mice as a tacrolimus receptor. FKBP12 作为他克莫司受体对硫酸钠葡聚糖诱导的小鼠溃疡性结肠炎的保护作用

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2025-01-01 Epub Date: 2024-03-11 DOI: 10.1080/15257770.2024.2320817

Birong Wang, Tingzan Li, Liqin Xu, Yuxi Cai

{"title":"Protective effect of FKBP12 on dextran sulfate sodium-induced ulcerative colitis in mice as a tacrolimus receptor.","authors":"Birong Wang, Tingzan Li, Liqin Xu, Yuxi Cai","doi":"10.1080/15257770.2024.2320817","DOIUrl":"10.1080/15257770.2024.2320817","url":null,"abstract":"Ulcerative colitis (UC) is a multifactorial intestinal disease with a high incidence. In recent years, there has been an urgent need for pleiotropic drugs with a clear biosafety profile. Tacrolimus (TAC) is an immunosuppressant with stronger in vivo effects and better gastrointestinal absorption and is considered a potential treatment for UC. FKBP12 is a mediator of TAC immunosuppression; however, it is unclear whether it can participate in the development of UC in combination with TAC. The purpose of this study is to preliminarily validate the function of FKBP12 by establishing dextran sulfate sodium (DSS)-induced UC model and TAC treatment. The results revealed that TAC was effective in alleviating DSS-induced UC symptoms such as body weight and disease activity index (DAI). TAC significantly protects colonic tissue and attenuates DSS-induced histomorphological changes. In addition, FKBP12 is down-regulated in the intestinal tissue of DSS-induced UC mice and in serum samples of UC patients. In conclusion, our study revealed that FKBP12 may act as a TAC receptor to have anti-inflammatory and protective effects on DSS-induced UC in mice, which will provide a new option for the treatment of UC.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"206-221"},"PeriodicalIF":1.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140102076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Deprotection of N1-methyladenosine-containing RNA using triethylamine hydrogen fluoride. 使用三乙胺氟化氢对含 N1-甲基腺苷的 RNA 进行脱保护。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2025-01-01 Epub Date: 2024-05-12 DOI: 10.1080/15257770.2024.2353181

A Apostle, S Fang

{"title":"Deprotection of N1-methyladenosine-containing RNA using triethylamine hydrogen fluoride.","authors":"A Apostle, S Fang","doi":"10.1080/15257770.2024.2353181","DOIUrl":"10.1080/15257770.2024.2353181","url":null,"abstract":"The N1-methyladenosine (m1A) epigenetic modification exists in many RNAs and is related to many human diseases. Chemically synthesized RNAs containing the modification are required for projects aimed at studying biological processes, mechanisms, and pathogenesis related to m1A. Existing methods for the synthesis of m1A containing RNAs use tetrabutylammonium fluoride (TBAF) for the deprotection of the 2'-silyl protecting groups. Since TBAF is nonvolatile, and is relatively non-polar, its use in the desilylation of RNA requires repeated desalting, which is tedious and gives low yields. Here we report the use of the volatile and neat triethylamine hydrogen fluoride (TEA-HF) for desilylation of m1A RNA synthesis. We found that the method is much simpler, and-in our hands-give significantly higher yield of RNA. Two major concerns for m1A RNA synthesis are depurination and Dimroth rearrangement. HPLC and MALDI MS of the RNA indicated that depurination is not a problem for the new method. The absence of Dimroth rearrangement is proven by RNA digestion followed by HPLC analysis of the nucleosides.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"318-325"},"PeriodicalIF":1.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11554933/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140911755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Association between polymorphism at codon 469 of the ICAM-1 gene and Henoch-Schönlein purpura in an Iranian cohort. 伊朗队列中 ICAM-1 基因第 469 个密码子的多态性与白癜风之间的关系。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2025-01-01 Epub Date: 2024-04-27 DOI: 10.1080/15257770.2024.2334360

Shima Salehi, Amir Hozhabrpour, Somayeh Takrim Nojehdeh, Marzieh Mojbafan

引用次数: 0

Identification of CSNK1D and KLK6 as two common upregulated genes present in BRCA1 mutated triple-negative breast cancer and ovarian epithelial carcinoma. 确定 CSNK1D 和 KLK6 是 BRCA1 突变三阴性乳腺癌和卵巢上皮癌中两个常见的上调基因。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2025-01-01 Epub Date: 2024-05-23 DOI: 10.1080/15257770.2024.2357267

Fatima Lakis, Rita Ayoub, Wissam H Faour, Mohammad Makki, Hanane Yassine, Hussein Fayyad-Kazan, Fadi Abdel Sater

{"title":"Identification of CSNK1D and KLK6 as two common upregulated genes present in BRCA1 mutated triple-negative breast cancer and ovarian epithelial carcinoma.","authors":"Fatima Lakis, Rita Ayoub, Wissam H Faour, Mohammad Makki, Hanane Yassine, Hussein Fayyad-Kazan, Fadi Abdel Sater","doi":"10.1080/15257770.2024.2357267","DOIUrl":"10.1080/15257770.2024.2357267","url":null,"abstract":"Deficiency in the breast cancer type 1 (BRCA1) gene expression predisposes to triple-negative breast cancer (TNBC) and ovarian cancer (OC). We previously identified by Comparative Genomic Hybridization (CGH) array a gain in the 17q25.3 genomic region in 90% of the BRCA1 mutated TNBC tissues, where 17 genes were up-regulated. A second region (Chr19_45681759_54221324) was identified as the second most frequent gain in the BRCA1-mutated population and has not yet been described in the context of BRCA1 mutation. We thus aimed to validate the expression of the Casein kinase 1 delta (CSNK1D) gene of Chr17 in TNBC and OC cell lines and to investigate the expression of genes of Chr19 in TNBC cell lines and tissues as well as in OC cell lines. Expression level of the genes of the 17q25.3, 19q13.32,13.33 and 13.41 chromosomal regions was analyzed using RT-PCR in BRCA1 deficient TNBC and OC cell lines, as well as in 10 BRCA1-mutated TNBC tissues versus 10 wild type carriers. Our results revealed a significant upregulation of CSNK1D gene expression in BRCA1 deficient TNBC and OC cell lines when compared to control ones, and a significant aberration in the expression of the other six genes of Chr19 was observed. Interestingly, upregulation of kallikrein-related peptidase 6 (KLK6) was detected among the BRCA1 deficient TNBC (cell lines and tissues) and OC cell lines. In conclusion, our results suggested that CSNK1D and KLK6 expression levels could be very promising in the search for biomarkers for BRCA1 deficient TNBC and OC.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"554-567"},"PeriodicalIF":1.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141088056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Prognostic significance of copper metabolism-related genes as risk markers in bladder urothelial carcinoma. 铜代谢相关基因作为膀胱尿路上皮癌风险标志物的预后意义

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2025-01-01 Epub Date: 2024-08-09 DOI: 10.1080/15257770.2024.2387783

Jiamo Zhang, Houwei Yang, Xuan Zhang, Jiangchuan Chen, Huaming Luo, Changlong Li, Xin Chen

{"title":"Prognostic significance of copper metabolism-related genes as risk markers in bladder urothelial carcinoma.","authors":"Jiamo Zhang, Houwei Yang, Xuan Zhang, Jiangchuan Chen, Huaming Luo, Changlong Li, Xin Chen","doi":"10.1080/15257770.2024.2387783","DOIUrl":"10.1080/15257770.2024.2387783","url":null,"abstract":"Bladder urothelial carcinoma (BLCA), a prevalent malignant neoplasm affecting the human urinary system, is frequently linked with an unfavorable prognosis in a significant proportion of individuals. More effective and sensitive markers are needed to provide a reference for prognostic judgment. We obtained RNA sequencing data and clinical information of individuals from TCGA, and 133 copper metabolism-related genes from literature. Prognostic genes were evaluated by univariate/multivariate Cox regression analysis and LASSO analysis, and a risk-scoring model was established and validated in the GEO dataset. The CIBERSORT method was utilized to explore immune cell infiltration in BLCA individuals. In addition, tumor immune dysfunction and exclusion (TIDE) and immunophenoscore (IPS) were utilized to verify whether the model can foretell the response of BLCA individuals to immunotherapy. We successfully constructed an 8-gene risk scoring model to foretell individuals' overall survival, and the model performed well in TCGA training and GEO validation cohorts. Lastly, a nomogram containing clinical parameters and risk scores was constructed to help individualized result prediction for individuals. Calibration curves demonstrated a high degree of concordance between the observed and projected survival durations, attesting to its exceptional predictive accuracy. Analysis utilizing CIBERSORT unveiled elevated levels of immune cell infiltration in individuals classified as low risk. TIDE and IPS analyses substantiated that low-risk individuals exhibited a more favorable response to immunotherapy. In summary, the model held immense potential for stratifying the risk of survival and guiding tailored treatment approaches for individuals with BLCA, thereby offering valuable insights for personalized therapeutic interventions.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"598-616"},"PeriodicalIF":1.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141907243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Optimization of microRNA extraction from the plasma of the common carp. 优化从鲤鱼血浆中提取 microRNA 的方法。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2025-01-01 Epub Date: 2024-09-05 DOI: 10.1080/15257770.2024.2400200

Yiwen Wan, Xiaoling Li, Xiangyi Chen, Yong He, Wenwen Suo, Xiao Yang, Zhonggui Xie

{"title":"Optimization of microRNA extraction from the plasma of the common carp.","authors":"Yiwen Wan, Xiaoling Li, Xiangyi Chen, Yong He, Wenwen Suo, Xiao Yang, Zhonggui Xie","doi":"10.1080/15257770.2024.2400200","DOIUrl":"10.1080/15257770.2024.2400200","url":null,"abstract":"Efficient and safe extraction of microRNAs (miRNAs) from biological samples is pivotal for genetic regulation studies and biotechnological applications. This study focuses on optimizing the microRNA extraction process from the plasma of common carp, a significant species in aquaculture. Recognizing the limitations and hazards of commercial extraction kits, which often employ toxic chemicals like phenol and chloroform, we sought to develop a safer and more effective alternative. Our optimized protocol utilizes guanidinium isothiocyanate (GITC) and sarkosyl, omitting hazardous substances. We explored several parameters including GITC concentration, the addition of sarkosyl, and the role of sodium chloride in enhancing miRNA yield. Our findings demonstrate that optimal conditions involve a GITC concentration of 4.2 M, a 3% sarkosyl concentration, and the use of sodium chloride at 0.5 M. We also investigated the utility of glycogen as a nucleic acid carrier, finding 160 µg to be the optimal concentration. Comparative analysis with commercial kits indicated our method provides higher miRNA yields with reduced cycle threshold values, underscoring the effectiveness of our custom protocol. This optimized approach not only enhances miRNA recovery but also emphasizes safety and cost-effectiveness, making it a valuable method for both research and practical applications in aquaculture.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"678-696"},"PeriodicalIF":1.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142133281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrated bioinformatics analysis of ferroptosis-related gene signature in inflammation and immunity in intervertebral disc degeneration. 椎间盘退变性炎症和免疫中铁蛋白相关基因特征的综合生物信息学分析。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2025-01-01 Epub Date: 2024-03-26 DOI: 10.1080/15257770.2024.2332403

Wei Liu, Hui-Min Li, Guangchao Bai

{"title":"Integrated bioinformatics analysis of ferroptosis-related gene signature in inflammation and immunity in intervertebral disc degeneration.","authors":"Wei Liu, Hui-Min Li, Guangchao Bai","doi":"10.1080/15257770.2024.2332403","DOIUrl":"10.1080/15257770.2024.2332403","url":null,"abstract":"Ferroptosis has recently been shown to play a significant role in the progression of intervertebral disk degeneration (IDD), although the underlying mechanism is still unknown. The objective of this work was to use stringent bioinformatic techniques to clarify the crucial roles played by genes associated with ferroptosis in the emergence of IDD. For additional study, the microarray data pertinent to the IDD were acquired from the Gene Expression Omnibus database. The ferroptosis-related and IDD-related genes (FIDDRGs) were identified using a variety of bioinformatic techniques, which were also used to carry out function enrichment analysis, protein-protein correlation analysis, build the correlation regulatory network, and examine the potential connections between ferroptosis and immune abnormalities and inflammatory responses in IDD. A total of 16 FIDDRGs were eliminated for the further function enrichment analysis, and 10 hub FIDDRGs were chosen to build the correlation regulatory network. Hub FIDDRGs were shown to be highly associated with M2 macrophages and hub inflammatory response-related genes in IDD. When seen as a whole, our findings can give fresh perspectives on the mechanistic studies of ferroptosis in the emergence of IDD and new prospective targets for the therapeutic approaches.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"238-258"},"PeriodicalIF":1.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140294075","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

MicroRNA-138 inhibits hypoxia-inducible factor 1α expression in breast cancer cells. MicroRNA-138 可抑制乳腺癌细胞中缺氧诱导因子 1α 的表达。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2025-01-01 Epub Date: 2024-07-14 DOI: 10.1080/15257770.2024.2351134

Mohammad Fayyad-Kazan, Rim ElDirani, Michella Ghassibe-Sabbagh, Eva Hamade, Nader Hadifeh, Rania El Majzoub, Hussein Fayyad-Kazan, Bassam Badran

{"title":"MicroRNA-138 inhibits hypoxia-inducible factor 1α expression in breast cancer cells.","authors":"Mohammad Fayyad-Kazan, Rim ElDirani, Michella Ghassibe-Sabbagh, Eva Hamade, Nader Hadifeh, Rania El Majzoub, Hussein Fayyad-Kazan, Bassam Badran","doi":"10.1080/15257770.2024.2351134","DOIUrl":"10.1080/15257770.2024.2351134","url":null,"abstract":"Background: Hypoxia, a critical feature during cancer development, leads to the stabilization and activation of the hypoxia-inducible factor 1-alpha (HIF-1α) to drive the expression of many target genes which in turn can promote many aspects of breast cancer biology, mainly metastasis and resistance to therapy. MicroRNAs are known to modulate the expression of many genes involved in breast cancer tumorigenesis. In this study, we examined the regulatory effect of miRNAs on HIF1α expression.Methods: MCF-7 and MDA-MB-231 were cultivated under normoxia or hypoxia conditions. TaqMan-Low Density Array (TLDA) was used to characterize the miRNA signatures. Wild-Type (WT) or mutated fragments of HIF-1α 3'UTR containing the miR-138 potential target site were cloned downstream of the Renilla luciferase gene in the psiCHECK-1 plasmid. Luciferase assays were then carried out. A lentiviral vector containing copGFP as a reporter gene was prepared and transduced into MCF-7 and MDA-MB-231 cells to assess the effect of identified deregulated miRNAs on HIF-1α expression.Results: Under hypoxic conditions, MCF-7 cells showed deregulated expression for 12 miRNAs. In the case of MDA-MB-231 cells, 16 miRNAs were deregulated in response to hypoxia. Interestingly, miR-138 that was downregulated in both MCF-7 and MDA-MB-231 cells cultivated under hypoxic conditions appeared to have a binding site in 3'UTR of HIF-1α. Moreover, our results indicated that miR-138 could down regulate HIF-1α expression, upon binding directly to its 3'UTR.Conclusions: Interestingly, our data highlights miR-138 as a potential therapeutic target to reduce HIF-1α expression and subsequently restrain breast cancer invasion and metastasis.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"302-317"},"PeriodicalIF":1.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141616899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Investigation of bisindole-linked pyrimidine moieties: synthesis using strantium-aluminum supported strontium aluminate nanophosphors catalyst, DNA reactivity, and in silico molecular docking studies. 双吲哚连接嘧啶分子的研究：使用铝酸锶纳米磷酸盐催化剂合成、DNA 反应性和分子对接研究。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2025-01-01 Epub Date: 2024-05-30 DOI: 10.1080/15257770.2024.2358901

Hanumesh, M K Amshumali, P Prachi, K Yogendra, N Madhusudhana, B Vinay Kumar

{"title":"Investigation of bisindole-linked pyrimidine moieties: synthesis using strantium-aluminum supported strontium aluminate nanophosphors catalyst, DNA reactivity, and in silico molecular docking studies.","authors":"Hanumesh, M K Amshumali, P Prachi, K Yogendra, N Madhusudhana, B Vinay Kumar","doi":"10.1080/15257770.2024.2358901","DOIUrl":"10.1080/15257770.2024.2358901","url":null,"abstract":"In this communication, an innovative and straightforward protocol for the one-pot catalytic synthesis of bis(indolyl)pyrimidine derivatives and their DNA binding abilities is presented. The synthesis involves the condensation of indole with diverse substituted pyrimidine-5-carbaldehydes, employing cost-effective and reusable Sr-Al supported nanophosphors, specifically strontium aluminate (SrAl2O4), as a catalyst. In particular, this method does not require the use of toxic solvents. The Sr-Al supported nanophosphorus catalyst exhibited sustained activity over multiple cycles and showed no significant decline while maintaining its strictly heterogeneous properties. The bis(indolyl)pyrimidine derivatives were extensively characterized using spectroscopic and analytical techniques. Furthermore, the interaction between these derivatives and CT-DNA was investigated by absorption spectroscopy, viscosity measurement, and in silico molecular docking studies. Photoinduced cleavage studies demonstrated the photonuclease activity of the compound against pUC19 DNA upon exposure to UV-visible radiation.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"456-473"},"PeriodicalIF":1.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141179274","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0